ClinVar Genomic variation as it relates to human health
NM_003781.4(B3GALNT1):c.537dup (p.Asp180fs)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_003781.4(B3GALNT1):c.537dup (p.Asp180fs)
Variation ID: 6634 Accession: VCV000006634.1
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 3q26.1 3: 161086217-161086218 (GRCh38) [ NCBI UCSC ] 3: 160804005-160804006 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Apr 4, 2013 Aug 16, 2002 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_003781.4:c.537dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_003772.1:p.Asp180fs frameshift NM_001038628.2:c.537dup NP_001033717.1:p.Asp180fs frameshift NM_001349130.2:c.537dup NP_001336059.1:p.Asp180fs frameshift NM_001349131.2:c.537dup NP_001336060.1:p.Asp180fs frameshift NM_001349132.2:c.537dup NP_001336061.1:p.Asp180fs frameshift NM_001349133.2:c.537dup NP_001336062.1:p.Asp180fs frameshift NM_001349134.2:c.537dup NP_001336063.1:p.Asp180fs frameshift NM_001349135.2:c.537dup NP_001336064.1:p.Asp180fs frameshift NM_001349136.2:c.537dup NP_001336065.1:p.Asp180fs frameshift NM_001349137.2:c.537dup NP_001336066.1:p.Asp180fs frameshift NM_001349138.2:c.537dup NP_001336067.1:p.Asp180fs frameshift NM_001349139.2:c.537dup NP_001336068.1:p.Asp180fs frameshift NM_001349140.2:c.537dup NP_001336069.1:p.Asp180fs frameshift NM_001349141.2:c.537dup NP_001336070.1:p.Asp180fs frameshift NM_001349142.2:c.537dup NP_001336071.1:p.Asp180fs frameshift NM_001349143.2:c.537dup NP_001336072.1:p.Asp180fs frameshift NM_001349144.2:c.537dup NP_001336073.1:p.Asp180fs frameshift NM_001349145.2:c.537dup NP_001336074.1:p.Asp180fs frameshift NM_001349146.2:c.537dup NP_001336075.1:p.Asp180fs frameshift NM_001349147.2:c.537dup NP_001336076.1:p.Asp180fs frameshift NM_001349148.2:c.537dup NP_001336077.1:p.Asp180fs frameshift NM_001349149.2:c.537dup NP_001336078.1:p.Asp180fs frameshift NM_001349150.2:c.537dup NP_001336079.1:p.Asp180fs frameshift NM_001349151.2:c.537dup NP_001336080.1:p.Asp180fs frameshift NM_001349152.2:c.537dup NP_001336081.1:p.Asp180fs frameshift NM_001349153.2:c.537dup NP_001336082.1:p.Asp180fs frameshift NM_001349154.2:c.537dup NP_001336083.1:p.Asp180fs frameshift NM_001349155.2:c.537dup NP_001336084.1:p.Asp180fs frameshift NM_001349156.2:c.537dup NP_001336085.1:p.Asp180fs frameshift NM_001349157.2:c.537dup NP_001336086.1:p.Asp180fs frameshift NM_001349158.2:c.537dup NP_001336087.1:p.Asp180fs frameshift NM_001349159.2:c.537dup NP_001336088.1:p.Asp180fs frameshift NM_001349160.1:c.537dup NP_001336089.1:p.Asp180fs frameshift NM_001349161.2:c.537dup NP_001336090.1:p.Asp180fs frameshift NM_001349162.2:c.897dup NP_001336091.1:p.Asp300fs frameshift NM_001349163.2:c.897dup NP_001336092.1:p.Asp300fs frameshift NM_033167.3:c.537dup NP_149357.1:p.Asp180fs frameshift NM_033168.3:c.537dup NP_149358.1:p.Asp180fs frameshift NM_033169.3:c.537dup NP_149359.1:p.Asp180fs frameshift NC_000003.12:g.161086218dup NC_000003.11:g.160804006dup NG_007854.1:g.24155dup LRG_820:g.24155dup LRG_820t1:c.537dup LRG_820p1:p.Asp180fs LRG_820t2:c.537dup LRG_820p2:p.Asp180fs - Protein change
- D180fs, D300fs
- Other names
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B3GALT3, 1-BP INS, 537A
- Canonical SPDI
- NC_000003.12:161086217:T:TT
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
- Links
- Comment on variant
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| B3GALNT1 | - | - |
GRCh38 GRCh37 |
22 | 46 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Affects (1) |
no assertion criteria provided
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Aug 16, 2002 | RCV000007013.3 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Affects
(Aug 16, 2002)
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no assertion criteria provided
Method: literature only
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P1PK BLOOD GROUP SYSTEM, P(k) PHENOTYPE
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000027209.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
In a blood sample from an Arabian patient with the P(2)(k) phenotype of the P1PK blood group system (see 111400), Hellberg et al. (2002) identified … (more)
In a blood sample from an Arabian patient with the P(2)(k) phenotype of the P1PK blood group system (see 111400), Hellberg et al. (2002) identified a homozygous 1-bp insertion, 537-538insA, resulting in a frameshift and a premature stop at codon 182. The mutation was predicted to truncate the protein to 55% of its native length, thereby rendering the enzyme nonfunctional. (less)
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Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Molecular basis of the globoside-deficient P(k) blood group phenotype. Identification of four inactivating mutations in the UDP-N-acetylgalactosamine: globotriaosylceramide 3-beta-N-acetylgalactosaminyltransferase gene. | Hellberg A | The Journal of biological chemistry | 2002 | PMID: 12023287 |
Text-mined citations for rs751995528 ...
HelpRecord last updated Apr 25, 2022
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
ClinGen staff contributed the HGVS expression for this variant.